Project title: Form and function of our Janus faced genome The conversion of RNA into DNA via reverse transcription has transformed the human genome: insertion of RNA-derived DNA copies has roughly doubled the mass of our hereditary material. However, integration of reverse transcribed RNAs is an inefficient process, even for the most successful genomic parasites (e.g. retroviruses, retrotransposons, and pseudogenes). The reverse transcribed copies that fail to integrate may be considered microcosms of the Roman god Janus: with one face, they gaze towards the past as an imperfect copy of a previous life (i.e. the RNA they are derived from), and with another face, they look towards the future, capable of directing the fate of their molecular environment. Remarkably, the identity and function of these genomic misfits that lie outside the confines of the traditional landscape of DNA is largely unexplored, but expected to be vast and powerful. We find that endogenous cDNA formation (i.e. reverse transcribed DNA derived from host RNA) is robust and has important biological and disease-modifying function. Blocking reverse transcription prevents endogenous cDNA formation, and interestingly, also blocks an endogenous cDNA-mediated mouse model of blindness. Here, we will extend these observations to systematically analyze the host-derived reverse transcriptome to produce the first draft atlas of the identity and function of endogenous cDNA, in health and disease. We will also experimentally demonstrate the relevance of endogenous cDNA to molecular and metabolic pathways, and provide an alternate explanation of toxicity attributed nucleoside reverse transcriptase inhibitors (e.g. peripheral neuropathy and developmental defects). We expect our work to demonstrate that the collision of host-derived RNA and the bidirectional flow of genetic information produces a powerful regulatory class of hereto underappreciated molecules that control health and disease, and can be harnessed to understand and manipulate basic tenets of cellular biology.